Welcome aboard, Matt. If you have a 390 GT engine in the Mustang, the exhaust ports are physically lower on the heads than they would be on an earlier FE engine, or on a 428 Cobra Jet engine. Difference in the port heights is around 1/2", if I recall correctly. If you try to put headers for the higher exhaust ports on heads with the lower port location, you will get an exhaust leak. Vice versa is the same way.
There are ways around this, such as slotting the bolt holes of the headers to make them move around on the head and allow them to fit. But its probably best to get the headers that were designed to fit your heads. One header manufacturer that I know of, FPA, makes both low port and high port style headers for early Mustangs. So, you just need to figure out what you've got for heads, and you can get the right headers.